[Bioperl-l] reading blast report
jason at bioperl.org
Thu Jan 14 16:28:29 EST 2010
On Jan 14, 2010, at 12:15 PM, Siddhartha Basu wrote:
> On Thu, 14 Jan 2010, Jason Stajich wrote:
>> What aspects of the report are you loading? You might consider the
>> report as tab-delimited (-m 8 format) if you only are interested in
>> start/end positions and scores of ailgnments which is a simpler and
>> dataset that has lower memory footprint by the parser.
> I think this would be a better approach i am mostly interested in
> start/end/score data only.
>> Searchio (default) -format => blast - you can try the BLAST -format
>> blast_pull instead which lazy parses to create objects and will
>> memory consumption.
> It's another good option though. But just out of curosity, so the
> regular blast parser do load the entire file in the memory consider
> output consist of multiple Results concatenated together into a
> single file. Could anybody clarify.
Each result is parsed (1 result per query) and all the hits and HSPs
are parsed and brought into memory with the standard (non-pull)
The SearchIO iterates at the level of result - that is why you call
next_result which parses each one at a time.
>> On Jan 14, 2010, at 11:15 AM, Siddhartha Basu wrote:
>>> I have a script that reads a tblastn report(13000 records) and
>>> loads in
>>> a chado database(Bio::Chado::Schema module), however the machine
>>> runs of
>>> memory. I am trying to figure
>>> out other than loading the database stuff
>>> if it the reading of SearchIO module could consume a lot of
>>> memory. So,
>>> when i am reading a blast file and getting the result object ....
>>> while (my $result = $searchio->next_result)
>>> * Does the searchio object loads a huge chunk of file in the
>>> memory or
>>> for each iteration it only reads a part of the result.
>>> * Does doing an index on blast report and then reading from it be
>>> faster and why. And is there any way i could iterate through each
>>> record in the index, will that be helpful.
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
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jason at bioperl.org
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